There is growing consensus that the optimization of the kinetic parameters for drug-protein binding leads to improved drug efficacy. Therefore, computational methods have been developed to predict kinetic rates and to derive quantitative structure-kinetic relationships (QSKRs). Many of these methods are based on crystal structures of ligand-protein complexes. However, a drawback is that each protein-ligand complex is usually treated as having a single structure. Here, we present a modification of COMparative BINding Energy (COMBINE) analysis, which uses the structures of protein-
ligand complexes to predict binding parameters. We introduce the option to use multiple structures to describe each ligand-protein complex into COMBINE analysis and
apply this to study the effects of protein flexibility on the derivation of dissociation rate constants (koff) for inhibitors of p38 mitogen-activated protein (MAP) kinase, which has a flexible binding site. Multiple structures were obtained for each ligand-protein complex by performing docking to an ensemble of protein configurations obtained from molecular dynamics simulations. Coefficients to scale ligand-protein interaction energies determined from energy-minimized structures of ligand-protein complexes were obtained by partial least squares regression and allowed the computation of koff values. The QSKR model obtained using single, energy minimized crystal structures for each ligand-protein complex had a higher predictive power than the QSKR model obtained with multiple structures from ensemble docking. However, the incorporation of protein-ligand flexibility helped to highlight additional ligand-protein interactions that lead to longer residence times, like interactions with residues Arg67 and Asp168, which are close to the ligand in many crystal structures, showing that COMBINE analysis is a promising method to design leads with improved kinetic rates for flexible proteins.